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Sodium in PDB 4o47: Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III

Enzymatic activity of Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III

All present enzymatic activity of Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III:
3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III, PDB code: 4o47 was solved by A.M.Schalk, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.73 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.872, 114.872, 138.971, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III (pdb code 4o47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III, PDB code: 4o47:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o47

Go back to Sodium Binding Sites List in 4o47
Sodium binding site 1 out of 2 in the Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:36.0
occ:1.00
O A:HIS65 2.2 32.0 1.0
O A:ALA63 2.4 31.4 1.0
O A:ASP58 2.4 33.1 1.0
O A:GLU56 2.5 32.6 1.0
O A:PHE61 2.6 33.7 1.0
O A:LEU55 2.9 34.3 1.0
C A:GLU56 3.2 34.4 1.0
C A:ASP58 3.3 35.6 1.0
C A:HIS65 3.3 32.5 1.0
CA A:GLU56 3.5 31.1 1.0
C A:ALA63 3.6 29.3 1.0
C A:PHE61 3.6 33.1 1.0
C A:LEU55 3.9 33.9 1.0
N A:HIS65 3.9 29.6 1.0
N A:ASP58 3.9 34.0 1.0
N A:ALA63 4.0 29.3 1.0
N A:ALA59 4.0 37.7 1.0
N A:PHE61 4.1 33.7 1.0
CA A:HIS65 4.1 31.7 1.0
CA A:ALA59 4.1 36.2 1.0
N A:GLU56 4.2 28.9 1.0
CA A:PHE61 4.2 34.3 1.0
C A:GLY64 4.2 29.6 1.0
CB A:PHE61 4.2 33.7 1.0
CA A:ASP58 4.2 36.9 1.0
N A:ASP57 4.2 35.9 1.0
N A:GLY66 4.3 34.6 1.0
C A:ASP57 4.3 36.6 1.0
CA A:ALA63 4.4 30.7 1.0
CA A:GLY66 4.4 31.6 1.0
N A:GLY64 4.5 27.9 1.0
CB A:HIS65 4.6 32.7 1.0
C A:ALA59 4.6 35.1 1.0
CA A:GLY64 4.6 28.2 1.0
O A:GLY64 4.7 29.3 1.0
N A:ASN62 4.7 28.7 1.0
CB A:ALA63 4.7 30.7 1.0
CA A:ASP57 4.8 37.6 1.0
O A:ASP57 4.8 37.3 1.0
CB A:GLU56 4.8 29.7 1.0
C A:GLY66 4.9 30.1 1.0
CB A:ASP58 4.9 35.8 1.0
O A:ALA59 5.0 38.4 1.0
N A:GLU60 5.0 34.8 1.0

Sodium binding site 2 out of 2 in 4o47

Go back to Sodium Binding Sites List in 4o47
Sodium binding site 2 out of 2 in the Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Uncleaved Guinea Pig L-Asparaginase Type III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:35.3
occ:1.00
O B:HIS65 2.2 35.2 1.0
O B:ALA63 2.3 36.2 1.0
O B:ASP58 2.4 37.5 1.0
O B:GLU56 2.5 41.0 1.0
O B:PHE61 2.6 36.2 1.0
O B:LEU55 2.7 36.8 1.0
C B:GLU56 3.3 38.7 1.0
C B:HIS65 3.4 34.9 1.0
C B:ASP58 3.4 37.2 1.0
C B:ALA63 3.5 35.9 1.0
C B:PHE61 3.6 40.6 1.0
CA B:GLU56 3.6 35.6 1.0
C B:LEU55 3.8 38.2 1.0
N B:ALA63 3.9 39.5 1.0
N B:ASP58 4.0 40.5 1.0
N B:HIS65 4.0 34.4 1.0
N B:PHE61 4.0 40.6 1.0
CB B:PHE61 4.1 40.9 1.0
CA B:PHE61 4.1 41.6 1.0
N B:GLU56 4.2 34.4 1.0
CA B:HIS65 4.2 34.4 1.0
CA B:ALA63 4.2 34.9 1.0
CA B:ASP58 4.2 39.5 1.0
C B:GLY64 4.3 36.7 1.0
N B:ALA59 4.3 37.4 1.0
N B:ASP57 4.3 37.8 1.0
N B:GLY66 4.3 36.6 1.0
CA B:ALA59 4.3 37.9 1.0
C B:ASP57 4.4 41.8 1.0
CA B:GLY66 4.4 42.5 1.0
N B:GLY64 4.5 37.4 1.0
CB B:ALA63 4.6 34.0 1.0
CA B:GLY64 4.6 37.4 1.0
C B:ALA59 4.6 40.2 1.0
CB B:HIS65 4.7 37.6 1.0
N B:ASN62 4.7 38.2 1.0
O B:GLY64 4.7 35.5 1.0
CB B:ASP58 4.8 42.3 1.0
CA B:ASP57 4.8 37.8 1.0
C B:GLY66 4.8 40.6 1.0
O B:ASP57 4.9 42.0 1.0
N B:GLU60 4.9 44.2 1.0
C B:ASN62 4.9 40.5 1.0
CB B:GLU56 5.0 38.1 1.0

Reference:

A.M.Schalk, A.Lavie. Structural and Kinetic Characterization of Guinea Pig L-Asparaginase Type III. Biochemistry V. 53 2318 2014.
ISSN: ISSN 0006-2960
PubMed: 24669941
DOI: 10.1021/BI401692V
Page generated: Tue Dec 15 06:56:24 2020

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